Xtal Waters and SolvateBox

From: Javier De Las Rivas <Javier.Rivas_at_physbio.mssm.edu>
Date: Tue 24 Oct 2000 16:04:46 +0100

A QUESTION ABOUT xleap and sander of AMBER7.0

I want to create with xLEAP a solvateBox around a protein that has 600 water
molecules in the crystal structure (1b6g), and I want to keep the water of the crystal.

How can I do that?

I have tried several times and xLEAP is not properly handeling the waters of the crystal.
There is some problem in the .top and .crd files obtained after using the "solvateBox" command,
because when I later run energy minimization with SANDER, the energy given is out of scale (too big).
But if I delete the waters of the crystal everything works fine.

Could you give me some answer to this problem

Dr. Javier De Las Rivas
Received on Tue Oct 24 2000 - 08:04:46 PDT
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